Hi everybody

I need to run a very large PSI-BLAST (using up to 10000 seqs and nr database) to extract PSSM but and I cannot use local PSI-BLAST because I ran out of RAM. So I used the web blast without problem but the PSSM is able to download only in ASN.1 format.

Reading here I have found that ASN.1 format is very hard to understand. Nevertheless I found I way to convert to ASCII, but I can retrieve only the 20 columns corresponding to the 20 Aa normalized scores per position in the PSSM. My problem is I need the information per position, and relative weight of gapless real matches to pseudocounts. These information is saved in the ASCII-PSSM of local blast (psiblast from ncbi-tools or blastpgp from blast) but is absent in ASN.1-PSSM from web blast.

So my questions are:

- is there a way to save ASCII-PSSM directly from web blast (this guide say it is possible, but seems to be an old document because it is not possible to follow the instructions there)

- is the information regarding information per position, and relative weight of gapless real matches to pseudocounts hidden in the ASN.1-PSSM from web blast

Thanks,